rnavar
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Published
20 hours ago •
nf-core
nf-core
STAR_ALIGN error "Not a valid S3 file system provider file attribute view: java.nio.file.attribute.BasicWithKeyFileAttributeView"
Description of the bug
Running nf-core/rnavar:1.0.0 with genome references from igenome or user-specified fasta/gtf files will both encounter the following error when in the STAR_ALIGN stage:
"Not a valid S3 file system provider file attribute view: java.nio.file.attribute.BasicWithKeyFileAttributeView"
Command used and terminal output
nextflow run nf-core/rnavar -r 1.0.0 \
--input /mnt/scratch/projects/adipocytes/samplesheet-bulkRNAseq-variant_calling.csv \
--outdir /mnt/scratch/projects/adipocytes/results/GRCh38-2023-A/rnaseq-variant_calling \
--genome GRCh38 \
--known_indels /mnt/scratch/projects/adipocytes/popscle/filtervcf.minAF.freemuxlet.vcf.gz \
--save_reference \
--max_cpus 30 \
--max_memory 235GB \
-resume \
-profile singularity
executor > local (5)
[- ] process > NFCORE_RNAVAR:RNAVAR:PREPAR... -
[- ] process > NFCORE_RNAVAR:RNAVAR:PREPAR... -
[- ] process > NFCORE_RNAVAR:RNAVAR:PREPAR... -
[41/23e647] process > NFCORE_RNAVAR:RNAVAR:INPUT_... [100%] 1 of 1, cached: 1 ✔
[- ] process > NFCORE_RNAVAR:RNAVAR:CAT_FASTQ -
[66/fea76f] process > NFCORE_RNAVAR:RNAVAR:FASTQC... [ 0%] 0 of 15
[- ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:MARKDU... -
[- ] process > NFCORE_RNAVAR:RNAVAR:MARKDU... -
[- ] process > NFCORE_RNAVAR:RNAVAR:MARKDU... -
[- ] process > NFCORE_RNAVAR:RNAVAR:MARKDU... -
[- ] process > NFCORE_RNAVAR:RNAVAR:MARKDU... -
[- ] process > NFCORE_RNAVAR:RNAVAR:SPLITN... -
[- ] process > NFCORE_RNAVAR:RNAVAR:SPLITN... -
[- ] process > NFCORE_RNAVAR:RNAVAR:SPLITN... -
[- ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:RECALI... -
[- ] process > NFCORE_RNAVAR:RNAVAR:RECALI... -
[- ] process > NFCORE_RNAVAR:RNAVAR:RECALI... -
[- ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:TABIX -
[- ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[- ] process > NFCORE_RNAVAR:RNAVAR:CUSTOM... -
[- ] process > NFCORE_RNAVAR:RNAVAR:MULTIQC -
Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
Error executing process > 'NFCORE_RNAVAR:RNAVAR:ALIGN_STAR:STAR_ALIGN (A20S35242OM)'
Caused by:
Not a valid S3 file system provider file attribute view: java.nio.file.attribute.BasicWithKeyFileAttributeView
Relevant files
No response
System information
- Nextflow version: 22.10.6
- Hardware: AWS EC2 - r5a instance type
- OS: Debian 11 x64
- Container engine: Singularity
- Executor: local
- nf-core/rnavar: 1.0.0
Is it resolved? I am also facing the same error message "Not a valid S3 file system provider file attribute view: java.nio.file.attribute.BasicWithKeyFileAttributeView"
